The U.S. District Court opened at Hartford, Connecticut, on November 19, 1839, to hear the case, but it adjourned to January because of the absence of certain cardinal witnesses. In the interim, the Spanish Minister pressed his claims once again, and Forsyth promised that he would get a ship ready to transport the captives to Cuba, should the verdict go against them, so that the abolitionists would have no time to appeal. When the Court resumed hearings on January 8, the U.S. Navy schooner Grampus was in the New Haven harbor on instructions of the President, who, many felt, "went to disgraceful extremes in his persistent attempts to thwart justice as promulgated by the courts." The three defense counsels urged the President not to have the case decided outside the courts "in the recesses of Cabinet, where these unfriended men can have no counsel and can produce no proof...." The abolitionists stood watch in shifts over the New Haven jail. They were afraid that the President might send men to seize the Amistad Africans even before the trial had concluded, and they were prepared to hide the captives, if necessary.

On January 13, 1840, Judge Judson finally rendered his verdict: the Amistad captives had been kidnapped and sold into slavery in violation of Spanish law; they were legally free and should, therefore, be transported back to Africa, whence they had been taken against their will. During the trial, Sengbe had made a favorable impression by giving detailed testimony through the interpreter, showing how he and his fellow Africans were kidnapped, bound, and mistreated. Emotion overcame him at one point, and Sengbe rose and shouted in English: "Give us free! Give us free!" But many people were against this freedom verdict, among them President Van Buren. He ordered District Attorney Holabird to appeal immediately against the decision.

Meanwhile, the Amistad captives were continuing with their classes in reading and writing and in the doctrines of Christianity. Despite their bitter disappointment at remaining in custody even after a favorable court decision, they still approached their studies with enthusiasm. The days began with James Covey translating Christian prayers into Mende, followed by a short sermon, and then instruction in the English language. The best pupil was eleven-year-old Kali, one of the four Amistad children, who learned to read and write with surprising speed. But all of the Amistad captives were keen to learn, and at times they grasped their Yale Divinity School teachers at the end of the day, pleading with them to stay just a bit longer. During this period little Kali wrote:

We talk American language a little, not very good. We write everyday; we write plenty letters; we read most all time; we read all Matthew and Mark and Luke and John, and plenty of little books. We love books very much.